The reason why the WEC did it was to prevent what was common in F1 and what Audi and Toyota did in 2012, where they spent most of the session in the garage or on pit road just waiting to run a fast lap and call it a day.

Granted, the averages deal IMO kinda sucks, but the only other way to make them run the whole session is to turn it into a practice session (like at LM) and don't have tires used in qualifying count towards the race provided that they start the race with the tires they used to set their fastest laps in Q.